title: Evaluating template-based and template-free protein-protein complex structure prediction.
abstract: We compared the performance of template-free (docking) and template-based methods for the prediction of protein-protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was allowed one prediction for each complex, but when the same number of predictions was allowed for each method, the docking approach outperformed template-based approaches. We identified strengths and weaknesses in each method. Template-based approaches were better able to handle complexes that involved conformational changes upon binding. Furthermore, the threading-based and docking methods were better than the structural-alignment-based method for enzyme-inhibitor complex prediction. Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy.
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, ASC-5th floor room 1069, 368 Plantation St., Worcester, MA 01605, USA. Zhiping.Weng@umassmed.edu.
authors.forename: Thom
authors.initials: T
authors.lastname: Vreven
authors.forename: Howook
authors.initials: H
authors.lastname: Hwang
authors.forename: Brian G
authors.initials: BG
authors.lastname: Pierce
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data*; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software; D040681:Structural Homology, Protein
keywords: COTH; PRISM; ZDOCK; protein–protein docking; protein–protein structure; template-based prediction